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- PDB-1y4l: Crystal structure of Bothrops asper myotoxin II complexed with th... -

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Basic information

Entry
Database: PDB / ID: 1y4l
TitleCrystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin
ComponentsPhospholipase A2 homolog 2
KeywordsHYDROLASE / Bothrops asper myotoxin II / anti-trypanosomal drug suramin
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / toxin activity / defense response to bacterium / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-SVR / Basic phospholipase A2 homolog 2
Similarity search - Component
Biological speciesBothrops asper (terciopelo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMurakami, M.T. / Arruda, E.Z. / Melo, P.A. / Martinez, A.B. / Calil-Elias, S. / Tomaz, M.A. / Lomonte, B. / Gutierrez, J.M. / Arni, R.K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Inhibition of Myotoxic Activity of Bothrops asper Myotoxin II by the Anti-trypanosomal Drug Suramin.
Authors: Murakami, M.T. / Arruda, E.Z. / Melo, P.A. / Martinez, A.B. / Calil-Elias, S. / Tomaz, M.A. / Lomonte, B. / Gutierrez, J.M. / Arni, R.K.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Remark 600HETEROGEN LIGAND P33 IS A FRAGMENT OF polyethyleneglycol 3350.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog 2
B: Phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,77910
Polymers27,5282
Non-polymers2,2518
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-25 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.199, 64.037, 85.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phospholipase A2 homolog 2 / Myotoxin II


Mass: 13764.138 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops asper (terciopelo) / Secretion: snake venom / References: UniProt: P24605, phospholipase A2
#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL, PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, isopropanol, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 30385 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.507 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.203 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23955 1537 5.1 %RANDOM
Rwork0.20563 ---
all0.227 30549 --
obs0.20734 28848 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.991 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--0.56 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 150 170 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222094
X-RAY DIFFRACTIONr_angle_refined_deg1.6632.0632794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52224.10378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77215382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0381510
X-RAY DIFFRACTIONr_chiral_restr0.1580.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021472
X-RAY DIFFRACTIONr_nbd_refined0.3320.31390
X-RAY DIFFRACTIONr_nbtor_refined0.3310.51427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.5361
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.530
X-RAY DIFFRACTIONr_mcbond_it1.27821214
X-RAY DIFFRACTIONr_mcangle_it2.08731884
X-RAY DIFFRACTIONr_scbond_it1.38421065
X-RAY DIFFRACTIONr_scangle_it2.1833910
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 104 -
Rwork0.312 2039 -
obs--96.97 %
Refinement TLS params.Method: refined / Origin x: 5.1713 Å / Origin y: 3.9203 Å / Origin z: 13.6086 Å
111213212223313233
T-0.0272 Å20.0017 Å20.0415 Å2-0.0033 Å20.0421 Å2---0.0144 Å2
L0.7816 °2-0.752 °20.6319 °2-0.9425 °2-0.474 °2--0.5926 °2
S0.0157 Å °-0.0314 Å °-0.0506 Å °-0.0427 Å °0.0088 Å °0.0075 Å °0.0279 Å °-0.0191 Å °-0.0244 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1331 - 121
2X-RAY DIFFRACTION1BB1 - 1331 - 121

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